I am encountering that if the App is in Background mode (not used or minimized in Dock) on Yosemite the Timer-Sequence stops – it is like OS X puts the Thread to sleep.
What Declare Function do I need to tell Yosemite that the running of my App is “critical” and should have a high priority?
I had an issue with Aeon Timer that stopped the timer when another app was run in full screen mode. It might be related. Try and build your app and see if the box appears. Also take a look at the links Michel provided above.